As you may know Google has updated PR for the website. We have also observed Google has updated Google Backlinks as well. Check your own and please share your thoughts if I am correct. * Condition is that you should have done real SEO efforts for your website. Hence you should only check those websites were you have performed SEO tasks.
Webmastertools somehow always shows only the very old backlinks (from sites that are down long ago) for me, and new ones, even those that are already up for over a month don't seem to be counted even though those sites appear updated in google search results